generate1.py

# pymol -c generate1.pyfrom chempy import io
from glob import glob
sys.path.append(".")
from pymol import cmd
import pymol
from pymol import cmd
def find_torsions(res_sele):
# this routine gets a list of atom ids which correspond to the# free torsions in the sidechain
res_sele = "("+res_sele+")"if cmd.count_atoms("(%s and n;N,CA)"%res_sele,quiet=1)<2:
return []
result = []
done = 0
# set up the starting trunk
cmd.select("trunk","(%s and n;N,CA,C,O)"%res_sele)
first_id = cmd.identify("(%s and n;N)"%res_sele)[0]
second_id = cmd.identify("(%s and n;CA)"%res_sele)[0]
to_do_list = [(first_id,second_id)]
while len(to_do_list):
(first_id,second_id) = to_do_list.pop(0)
# find candidates for the 3rd atom in the dihedral
cmd.select("candi","(%s and (neighbor trunk))"%res_sele)
pymol.stored.list = []
cmd.iterate("candi","stored.list.append((name,ID))")
candi_list = pymol.stored.list
if len(candi_list):
# we may have a dihedral
dihe_list = []
for a in candi_list:
if cmd.select("termi","(%s and (not trunk) and (neighbor id %d))"%
(res_sele,a[1]))>0:
# apparently we do, but is it acyclic# (i.e., can edit split the molecule?)
cmd.edit("(%s and trunk and (neighbor id %d))"%(res_sele,a[1]),
"(%s and id %d)"%(res_sele,a[1]))
if'pkfrag2'in cmd.get_names('selections'):
# yes, so this is a valid dihedral
dihe_list.append(a)
else:
# no, so add the third atom to the trunk
cmd.select("trunk","(trunk or (%s and id %d))"%(res_sele,a[1]))
else:
# no fourth atom, so add this atom to the trunk
cmd.select("trunk","(trunk or (%s and id %d))"%(res_sele,a[1]))
if len(dihe_list):
# choose 3rd atom using alphanumeric order
dihe_list.sort()
third_id = dihe_list[0][1]
# if there is another third atom, then repeat later if len(dihe_list)>1:
to_do_list.insert(0,(first_id,second_id))
# now choose the 4th atom, which we know exists, using a similar criterion
cmd.select("termi","(%s and (not trunk) and (neighbor id %d))"%
(res_sele,third_id))
pymol.stored.list=[]
cmd.iterate("termi","stored.list.append((name,ID))")
termi_list = pymol.stored.list
termi_list.sort()
fourth_id = termi_list[0][1]
# at this point, we should have a complete dihedral# add the third atom into the trunk, and store the second and third for# outward extension later on
to_do_list.append((second_id,third_id))
cmd.select("trunk","(trunk or (%s and id %d))"%(res_sele,third_id))
# cmd.show('sticks','(%s and (id %d,%d,%d,%d))'%# (res_sele,first_id,second_id,third_id,fourth_id))
result.append((first_id,second_id,third_id,fourth_id))
return result
def measure_all_torsions(sele,prot_dict):
id_list = cmd.identify("((%s) and name ca)"%sele)
for a in id_list:
res_sele = "(alt '' and (byres id %d) and (%s))"%(a,sele)
lst = find_torsions(res_sele)
if len(lst):
cmd.iterate("(%s and n;ca)"%res_sele,"stored.resn=resn")
resn = pymol.stored.resn
print resn
name_list = []
for a in lst:
pymol.stored.names = []
for b in a:
cmd.iterate("(%s and id %d)"%(res_sele,b),"stored.names.append(name)")
name_list.append(tuple(pymol.stored.names))
res_dict = {}
for a in name_list:
dihe = cmd.get_dihedral("(%s and name %s)"%(res_sele,a[0]),
"(%s and name %s)"%(res_sele,a[1]),
"(%s and name %s)"%(res_sele,a[2]),
"(%s and name %s)"%(res_sele,a[3]))
res_dict[a]=dihe
ifnot prot_dict.has_key(resn):
prot_dict[resn]=[]
prot_dict[resn].append(res_dict)
sc_dict = {}
cmd.feedback('disable','selector','result')
cmd.feedback('disable','executive','action')
for fyle in glob("source/*"):
cmd.load(fyle)
cmd.remove("(het)")
cmd.remove("(hydro or not alt '')")
cmd.remove("(byres b>25)") # only use well-defined residues
cmd.remove("(not (byres name ca))")
cmd.remove("(not (byres name n))")
cmd.remove("(not (byres name c))")
cmd.refresh()
measure_all_torsions("all",sc_dict)
cmd.delete("all")
#for a in sc_dict.keys():# print a,dict[a]#print len(dict.keys())
io.pkl.toFile(sc_dict,"sc_raw.pkl")